Multiple sequence alignment - TraesCS2B01G592500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G592500 chr2B 100.000 6191 0 0 1 6191 777512264 777518454 0.000000e+00 11433
1 TraesCS2B01G592500 chr2B 80.087 462 48 19 5749 6191 777361822 777362258 2.800000e-78 303
2 TraesCS2B01G592500 chr2D 96.123 5803 159 33 403 6191 634470554 634476304 0.000000e+00 9409
3 TraesCS2B01G592500 chr2D 78.795 448 50 23 5749 6184 634432473 634432887 6.160000e-65 259
4 TraesCS2B01G592500 chr2D 84.167 240 10 11 1 233 634469898 634470116 2.260000e-49 207
5 TraesCS2B01G592500 chr2A 93.378 6071 215 82 1 5989 778924555 778918590 0.000000e+00 8811
6 TraesCS2B01G592500 chr2A 78.289 456 50 25 5749 6189 779187959 779187538 1.330000e-61 248


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G592500 chr2B 777512264 777518454 6190 False 11433 11433 100.000 1 6191 1 chr2B.!!$F2 6190
1 TraesCS2B01G592500 chr2D 634469898 634476304 6406 False 4808 9409 90.145 1 6191 2 chr2D.!!$F2 6190
2 TraesCS2B01G592500 chr2A 778918590 778924555 5965 True 8811 8811 93.378 1 5989 1 chr2A.!!$R1 5988

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
155 162 0.321919 CGGATGGGATGGTGGCATAG 60.322 60.0 0.00 0.00 0.00 2.23 F
156 163 0.610232 GGATGGGATGGTGGCATAGC 60.610 60.0 0.00 0.00 0.00 2.97 F
1164 1465 0.041090 TCCCTCCCCAATTTCCTTGC 59.959 55.0 0.00 0.00 33.20 4.01 F
1169 1489 0.248289 CCCCAATTTCCTTGCTGCAG 59.752 55.0 10.11 10.11 33.20 4.41 F
2094 2420 0.322816 TTGAGCTGGGCTGTTCCATC 60.323 55.0 0.00 0.00 39.88 3.51 F
2581 2907 0.175760 TCTGGACGGTGATAGCAAGC 59.824 55.0 0.00 0.00 0.00 4.01 F
3968 4295 1.009829 GCTCCTAACATGGCAACTCG 58.990 55.0 0.00 0.00 37.61 4.18 F
5016 5345 0.469070 ATGCCATCTCAGAGCTGACC 59.531 55.0 2.62 0.00 35.46 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1146 1447 0.041684 AGCAAGGAAATTGGGGAGGG 59.958 55.000 0.00 0.00 39.47 4.30 R
1306 1632 0.169672 CTGCATCGCAAAGACAAGGG 59.830 55.000 0.00 0.00 38.41 3.95 R
1980 2306 0.324943 TGAGGCCCTTACAGCAGAAC 59.675 55.000 0.00 0.00 0.00 3.01 R
2511 2837 0.599728 GAGGCCAGCGAGATGACATC 60.600 60.000 5.01 7.39 0.00 3.06 R
3939 4266 1.429930 TGTTAGGAGCACCAGGACAA 58.570 50.000 2.07 0.00 38.94 3.18 R
4554 4882 3.015327 GACCATCTGCAGATCAGCTTTT 58.985 45.455 26.44 0.67 42.56 2.27 R
5085 5414 3.781770 GAGGGCGCCTGAGATGTCG 62.782 68.421 28.56 0.00 31.76 4.35 R
6126 6474 1.613255 GGCCAGATTTCTTGTTCCCGA 60.613 52.381 0.00 0.00 0.00 5.14 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 63 6.360618 GTTTGTCATCTCCCCTGATTATTCT 58.639 40.000 0.00 0.00 0.00 2.40
67 69 2.641815 CTCCCCTGATTATTCTCCCCAG 59.358 54.545 0.00 0.00 0.00 4.45
68 70 1.074566 CCCCTGATTATTCTCCCCAGC 59.925 57.143 0.00 0.00 0.00 4.85
70 72 2.377869 CCCTGATTATTCTCCCCAGCAT 59.622 50.000 0.00 0.00 0.00 3.79
128 135 1.983481 GCACACATGGCCATGGGAA 60.983 57.895 46.64 8.02 44.83 3.97
129 136 1.332144 GCACACATGGCCATGGGAAT 61.332 55.000 46.64 27.93 44.83 3.01
130 137 0.462375 CACACATGGCCATGGGAATG 59.538 55.000 46.64 34.98 44.83 2.67
131 138 0.688418 ACACATGGCCATGGGAATGG 60.688 55.000 46.64 28.54 44.83 3.16
132 139 1.075076 ACATGGCCATGGGAATGGG 60.075 57.895 41.25 20.21 42.91 4.00
133 140 1.839747 CATGGCCATGGGAATGGGG 60.840 63.158 34.31 8.65 41.94 4.96
134 141 2.019866 ATGGCCATGGGAATGGGGA 61.020 57.895 20.04 0.00 41.94 4.81
135 142 1.381900 ATGGCCATGGGAATGGGGAT 61.382 55.000 20.04 0.00 41.94 3.85
136 143 1.228988 GGCCATGGGAATGGGGATC 60.229 63.158 15.13 0.00 41.94 3.36
137 144 1.604593 GCCATGGGAATGGGGATCG 60.605 63.158 15.13 0.00 41.94 3.69
138 145 1.075482 CCATGGGAATGGGGATCGG 59.925 63.158 2.85 0.00 38.04 4.18
153 160 1.429543 ATCGGATGGGATGGTGGCAT 61.430 55.000 0.00 0.00 0.00 4.40
155 162 0.321919 CGGATGGGATGGTGGCATAG 60.322 60.000 0.00 0.00 0.00 2.23
156 163 0.610232 GGATGGGATGGTGGCATAGC 60.610 60.000 0.00 0.00 0.00 2.97
170 177 5.767168 GGTGGCATAGCAGATAGAGAAATTT 59.233 40.000 0.00 0.00 0.00 1.82
175 182 7.875041 GGCATAGCAGATAGAGAAATTTAGACA 59.125 37.037 0.00 0.00 0.00 3.41
177 184 9.755804 CATAGCAGATAGAGAAATTTAGACACA 57.244 33.333 0.00 0.00 0.00 3.72
178 185 9.757227 ATAGCAGATAGAGAAATTTAGACACAC 57.243 33.333 0.00 0.00 0.00 3.82
179 186 7.615403 AGCAGATAGAGAAATTTAGACACACA 58.385 34.615 0.00 0.00 0.00 3.72
180 187 7.547370 AGCAGATAGAGAAATTTAGACACACAC 59.453 37.037 0.00 0.00 0.00 3.82
181 188 7.331934 GCAGATAGAGAAATTTAGACACACACA 59.668 37.037 0.00 0.00 0.00 3.72
182 189 8.867935 CAGATAGAGAAATTTAGACACACACAG 58.132 37.037 0.00 0.00 0.00 3.66
324 362 2.041405 CCACCCTCTCCCTCTCCC 60.041 72.222 0.00 0.00 0.00 4.30
326 364 2.204705 ACCCTCTCCCTCTCCCCT 60.205 66.667 0.00 0.00 0.00 4.79
329 367 2.612251 CTCTCCCTCTCCCCTCCC 59.388 72.222 0.00 0.00 0.00 4.30
528 813 4.069232 CAGTGAGGCGCGGAGGAA 62.069 66.667 8.83 0.00 0.00 3.36
597 884 1.132201 TCCAGGGAAGGAAGGGAAAGA 60.132 52.381 0.00 0.00 33.93 2.52
598 885 1.710809 CCAGGGAAGGAAGGGAAAGAA 59.289 52.381 0.00 0.00 0.00 2.52
630 917 4.565531 ACGATTTGTCCGTCCGTC 57.434 55.556 0.00 0.00 34.97 4.79
631 918 1.080298 ACGATTTGTCCGTCCGTCC 60.080 57.895 0.00 0.00 34.97 4.79
724 1011 4.733542 ACGGGGCCGGATTTGGTG 62.734 66.667 18.95 0.00 44.69 4.17
798 1085 4.095211 GGAGTGGTTAGTTCTTCCCTACT 58.905 47.826 0.00 0.00 0.00 2.57
800 1087 4.095211 AGTGGTTAGTTCTTCCCTACTCC 58.905 47.826 0.00 0.00 0.00 3.85
837 1124 2.383527 GCGCTAGCTGCTTCGTTGT 61.384 57.895 19.70 0.00 41.01 3.32
839 1126 1.687494 CGCTAGCTGCTTCGTTGTCC 61.687 60.000 13.93 0.00 40.11 4.02
929 1226 1.148759 GAAGATCTGCGGCGGTTCTC 61.149 60.000 19.70 10.63 0.00 2.87
931 1228 4.514577 ATCTGCGGCGGTTCTCGG 62.515 66.667 9.78 0.00 39.69 4.63
957 1255 0.675522 TTTGGGCGGATTCGAGGAAC 60.676 55.000 0.00 0.00 39.00 3.62
1050 1348 2.552802 CTGCAAGGAGACCAAGCTG 58.447 57.895 0.00 0.00 0.00 4.24
1107 1405 0.877743 GCAAGCTCTCCAAGTTCACC 59.122 55.000 0.00 0.00 0.00 4.02
1131 1432 1.457455 CTCCAGCTCCTCCTCCTCC 60.457 68.421 0.00 0.00 0.00 4.30
1146 1447 3.432890 CCTCCTCCATGTAAGCCTTCTTC 60.433 52.174 0.00 0.00 33.85 2.87
1155 1456 0.776080 AAGCCTTCTTCCCTCCCCAA 60.776 55.000 0.00 0.00 0.00 4.12
1156 1457 0.553612 AGCCTTCTTCCCTCCCCAAT 60.554 55.000 0.00 0.00 0.00 3.16
1157 1458 0.336392 GCCTTCTTCCCTCCCCAATT 59.664 55.000 0.00 0.00 0.00 2.32
1161 1462 2.074922 TCTTCCCTCCCCAATTTCCT 57.925 50.000 0.00 0.00 0.00 3.36
1163 1464 2.042979 TCTTCCCTCCCCAATTTCCTTG 59.957 50.000 0.00 0.00 34.42 3.61
1164 1465 0.041090 TCCCTCCCCAATTTCCTTGC 59.959 55.000 0.00 0.00 33.20 4.01
1166 1467 1.188863 CCTCCCCAATTTCCTTGCTG 58.811 55.000 0.00 0.00 33.20 4.41
1169 1489 0.248289 CCCCAATTTCCTTGCTGCAG 59.752 55.000 10.11 10.11 33.20 4.41
1181 1501 1.168407 TGCTGCAGGTGCTCTGTTTC 61.168 55.000 17.12 0.00 45.08 2.78
1197 1517 5.591099 TCTGTTTCCTGCTGAATTTTGTTC 58.409 37.500 0.00 0.00 31.67 3.18
1224 1549 7.456902 TCCTTGGTTAATTAGTCTGGTCTTAGT 59.543 37.037 0.00 0.00 0.00 2.24
1225 1550 7.549488 CCTTGGTTAATTAGTCTGGTCTTAGTG 59.451 40.741 0.00 0.00 0.00 2.74
1226 1551 7.549147 TGGTTAATTAGTCTGGTCTTAGTGT 57.451 36.000 0.00 0.00 0.00 3.55
1230 1555 1.717032 AGTCTGGTCTTAGTGTGGCA 58.283 50.000 0.00 0.00 0.00 4.92
1273 1599 3.806316 TTAGCGCTGCTAGTTGTTTTC 57.194 42.857 22.90 0.00 42.34 2.29
1288 1614 1.264288 GTTTTCTGGTGTGAAGAGCCG 59.736 52.381 0.00 0.00 0.00 5.52
1290 1616 1.407656 TTCTGGTGTGAAGAGCCGGT 61.408 55.000 1.90 0.00 0.00 5.28
1294 1620 1.228657 GGTGTGAAGAGCCGGTTGAC 61.229 60.000 1.90 0.00 0.00 3.18
1299 1625 1.140052 TGAAGAGCCGGTTGACTCAAA 59.860 47.619 1.90 0.00 35.28 2.69
1301 1627 2.100605 AGAGCCGGTTGACTCAAATC 57.899 50.000 1.90 0.00 35.28 2.17
1305 1631 2.003301 GCCGGTTGACTCAAATCTCTC 58.997 52.381 1.90 0.00 0.00 3.20
1306 1632 2.622436 CCGGTTGACTCAAATCTCTCC 58.378 52.381 0.00 0.00 0.00 3.71
1396 1722 1.594034 CCGCTGACTACGTCGACATAC 60.594 57.143 17.16 2.56 34.95 2.39
1401 1727 0.737219 ACTACGTCGACATACTGGCC 59.263 55.000 17.16 0.00 0.00 5.36
1608 1934 0.973496 GAGGGGAGGAGCCGATATCC 60.973 65.000 0.00 0.00 37.63 2.59
1824 2150 3.194861 TCCACTGTATGCGATGCTTAAC 58.805 45.455 0.00 0.00 0.00 2.01
1869 2195 2.562738 TGAGGTCATTGACATGTCTCGT 59.437 45.455 25.55 9.54 35.97 4.18
1872 2198 5.105351 TGAGGTCATTGACATGTCTCGTAAT 60.105 40.000 25.55 14.22 35.97 1.89
1890 2216 0.407139 ATGGCATCTCCCCTATTGGC 59.593 55.000 0.00 0.00 35.41 4.52
1953 2279 5.986135 ACCGTATTTGTCAGCAGAATCTATC 59.014 40.000 0.00 0.00 0.00 2.08
1980 2306 5.803967 GGAGATGCTTGATTTTGCTAACAAG 59.196 40.000 0.00 0.00 41.46 3.16
2007 2333 0.466372 GTAAGGGCCTCAAGGATGCC 60.466 60.000 6.46 4.20 41.52 4.40
2046 2372 4.614946 CTTCTTTTGTTTCTTCCAGGCAG 58.385 43.478 0.00 0.00 0.00 4.85
2094 2420 0.322816 TTGAGCTGGGCTGTTCCATC 60.323 55.000 0.00 0.00 39.88 3.51
2164 2490 4.730657 CTTGAATGATGAGCAAGTGGTTC 58.269 43.478 0.00 0.00 35.49 3.62
2283 2609 0.512952 GTGCAACGTCAGATGTCACC 59.487 55.000 0.00 0.00 0.00 4.02
2319 2645 2.456119 GCTGGTTGACTCGGCATCG 61.456 63.158 0.00 0.00 36.58 3.84
2448 2774 1.681793 CATGTCTACTCGGTAGTGGGG 59.318 57.143 9.84 0.00 37.41 4.96
2511 2837 3.461061 TCTCAACTTGCTTGACTCTGTG 58.539 45.455 0.00 0.00 33.65 3.66
2523 2849 2.159324 TGACTCTGTGATGTCATCTCGC 60.159 50.000 13.90 5.29 38.15 5.03
2581 2907 0.175760 TCTGGACGGTGATAGCAAGC 59.824 55.000 0.00 0.00 0.00 4.01
3006 3332 2.962421 AGATGCTGCTAAGGGAGTACTC 59.038 50.000 14.87 14.87 33.26 2.59
3040 3366 7.398024 ACAATCTTTGCTACTTCTCAGGTAAT 58.602 34.615 0.00 0.00 0.00 1.89
3108 3435 8.764287 CATAATGCAGTTGTTAGTCGATCAATA 58.236 33.333 0.00 0.00 0.00 1.90
3112 3439 8.710835 TGCAGTTGTTAGTCGATCAATAATTA 57.289 30.769 0.00 0.00 0.00 1.40
3113 3440 9.157104 TGCAGTTGTTAGTCGATCAATAATTAA 57.843 29.630 0.00 0.00 0.00 1.40
3139 3466 4.948847 TGTAGATGCTACATCACATGGTC 58.051 43.478 10.02 0.00 33.60 4.02
3189 3516 6.171921 GCTAATTCAGTAGATGGCTGATCAT 58.828 40.000 0.00 0.00 41.87 2.45
3265 3592 6.699575 ATGTTAGGACTAATGCAATTGTCC 57.300 37.500 23.03 23.03 46.06 4.02
3354 3681 2.334946 GGCAAGCCAGCATGAACGA 61.335 57.895 6.14 0.00 39.69 3.85
3363 3690 3.119849 GCCAGCATGAACGACTTGTTTAT 60.120 43.478 0.00 0.00 42.09 1.40
3605 3932 5.923733 TTCTACACCTCTTTCTCAGATCC 57.076 43.478 0.00 0.00 0.00 3.36
3623 3950 1.843851 TCCGCCTGGATAAACATTCCT 59.156 47.619 0.00 0.00 40.17 3.36
3721 4048 9.309516 CCGTAAATACTTATGTAGCAAAGAAGA 57.690 33.333 0.00 0.00 31.51 2.87
3968 4295 1.009829 GCTCCTAACATGGCAACTCG 58.990 55.000 0.00 0.00 37.61 4.18
4554 4882 4.028131 AGTATTGTGACCGGGATCTAACA 58.972 43.478 6.32 0.00 0.00 2.41
4775 5103 2.646121 CCAGAGAGGGTTTGTTGGC 58.354 57.895 0.00 0.00 0.00 4.52
4822 5150 8.157476 CAGTTCCTAACATGGGCTAGTAATAAT 58.843 37.037 0.00 0.00 0.00 1.28
5016 5345 0.469070 ATGCCATCTCAGAGCTGACC 59.531 55.000 2.62 0.00 35.46 4.02
5025 5354 1.093159 CAGAGCTGACCAAGGCAATC 58.907 55.000 0.00 0.00 0.00 2.67
5055 5384 1.003233 GGACCTGAACCTGCTCCAC 60.003 63.158 0.00 0.00 0.00 4.02
5261 5590 5.041287 CCAGTGTATGTTCTGTACCATACG 58.959 45.833 12.46 0.00 34.32 3.06
5480 5810 4.327087 GCTGTTGTGTTCTTCAGTTTTTGG 59.673 41.667 0.00 0.00 0.00 3.28
5501 5831 3.055819 GGACTGCTGTAAGATCCACTTCA 60.056 47.826 0.00 0.00 39.72 3.02
5508 5838 5.182001 GCTGTAAGATCCACTTCATTTGTGT 59.818 40.000 0.00 0.00 39.72 3.72
5509 5839 6.294176 GCTGTAAGATCCACTTCATTTGTGTT 60.294 38.462 0.00 0.00 39.72 3.32
5510 5840 7.094805 GCTGTAAGATCCACTTCATTTGTGTTA 60.095 37.037 0.00 0.00 39.72 2.41
5511 5841 8.322906 TGTAAGATCCACTTCATTTGTGTTAG 57.677 34.615 0.00 0.00 39.72 2.34
5512 5842 7.936847 TGTAAGATCCACTTCATTTGTGTTAGT 59.063 33.333 0.00 0.00 39.72 2.24
5513 5843 9.431887 GTAAGATCCACTTCATTTGTGTTAGTA 57.568 33.333 0.00 0.00 39.72 1.82
5514 5844 7.907214 AGATCCACTTCATTTGTGTTAGTAC 57.093 36.000 0.00 0.00 33.92 2.73
5572 5909 5.114785 TGTCCATTGTGTAACCATTTTCG 57.885 39.130 0.00 0.00 34.36 3.46
5635 5972 4.749099 CAGGCTGCAGATGTAAAGATAGTC 59.251 45.833 20.43 0.00 0.00 2.59
5647 5984 9.250624 GATGTAAAGATAGTCCATGTAGTTGTC 57.749 37.037 0.00 0.00 0.00 3.18
5989 6330 8.989980 GGTATGCCACTCTAATCATAGTTAAAC 58.010 37.037 0.00 0.00 34.09 2.01
6041 6389 6.874288 AGGCTGATATAAGAAAGCATCAAC 57.126 37.500 0.00 0.00 37.40 3.18
6042 6390 5.468072 AGGCTGATATAAGAAAGCATCAACG 59.532 40.000 0.00 0.00 37.40 4.10
6044 6392 6.423905 GGCTGATATAAGAAAGCATCAACGTA 59.576 38.462 0.00 0.00 37.40 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.053627 GATGACAAACGCAAAAGGCAG 58.946 47.619 0.00 0.00 45.17 4.85
61 63 1.062364 GATGGATCTCATGCTGGGGA 58.938 55.000 1.91 0.00 35.97 4.81
128 135 1.210204 CCATCCCATCCGATCCCCAT 61.210 60.000 0.00 0.00 0.00 4.00
129 136 1.847506 CCATCCCATCCGATCCCCA 60.848 63.158 0.00 0.00 0.00 4.96
130 137 1.847968 ACCATCCCATCCGATCCCC 60.848 63.158 0.00 0.00 0.00 4.81
131 138 1.376466 CACCATCCCATCCGATCCC 59.624 63.158 0.00 0.00 0.00 3.85
132 139 1.376466 CCACCATCCCATCCGATCC 59.624 63.158 0.00 0.00 0.00 3.36
133 140 1.302832 GCCACCATCCCATCCGATC 60.303 63.158 0.00 0.00 0.00 3.69
134 141 1.429543 ATGCCACCATCCCATCCGAT 61.430 55.000 0.00 0.00 0.00 4.18
135 142 0.766288 TATGCCACCATCCCATCCGA 60.766 55.000 0.00 0.00 32.85 4.55
136 143 0.321919 CTATGCCACCATCCCATCCG 60.322 60.000 0.00 0.00 32.85 4.18
137 144 0.610232 GCTATGCCACCATCCCATCC 60.610 60.000 0.00 0.00 32.85 3.51
138 145 0.111061 TGCTATGCCACCATCCCATC 59.889 55.000 0.00 0.00 32.85 3.51
153 160 8.749354 TGTGTGTCTAAATTTCTCTATCTGCTA 58.251 33.333 0.00 0.00 0.00 3.49
155 162 7.331934 TGTGTGTGTCTAAATTTCTCTATCTGC 59.668 37.037 0.00 0.00 0.00 4.26
156 163 8.763049 TGTGTGTGTCTAAATTTCTCTATCTG 57.237 34.615 0.00 0.00 0.00 2.90
170 177 0.969149 CTGGGAGCTGTGTGTGTCTA 59.031 55.000 0.00 0.00 0.00 2.59
175 182 0.550914 TTTTCCTGGGAGCTGTGTGT 59.449 50.000 0.00 0.00 0.00 3.72
223 230 4.162690 CCGAGGCCGAGGGGAAAG 62.163 72.222 11.21 0.00 38.22 2.62
225 232 3.077529 TATCCGAGGCCGAGGGGAA 62.078 63.158 17.65 1.37 38.22 3.97
227 234 3.303928 GTATCCGAGGCCGAGGGG 61.304 72.222 17.65 8.62 38.22 4.79
228 235 3.303928 GGTATCCGAGGCCGAGGG 61.304 72.222 17.65 11.02 38.22 4.30
231 238 2.836360 GTGGGTATCCGAGGCCGA 60.836 66.667 0.00 0.00 38.22 5.54
232 239 3.925090 GGTGGGTATCCGAGGCCG 61.925 72.222 0.00 0.00 35.24 6.13
233 240 3.557290 GGGTGGGTATCCGAGGCC 61.557 72.222 0.00 0.00 35.24 5.19
234 241 3.557290 GGGGTGGGTATCCGAGGC 61.557 72.222 0.00 0.00 35.24 4.70
309 347 2.204705 AGGGGAGAGGGAGAGGGT 60.205 66.667 0.00 0.00 0.00 4.34
312 350 2.612251 GGGAGGGGAGAGGGAGAG 59.388 72.222 0.00 0.00 0.00 3.20
572 858 3.009115 TTCCTTCCCTGGAGCGGG 61.009 66.667 0.00 0.00 46.13 6.13
587 873 2.162408 CCAAGATGCGTTCTTTCCCTTC 59.838 50.000 0.00 0.00 42.15 3.46
597 884 0.320374 TCGTCCTTCCAAGATGCGTT 59.680 50.000 0.00 0.00 0.00 4.84
598 885 0.537188 ATCGTCCTTCCAAGATGCGT 59.463 50.000 0.00 0.00 0.00 5.24
679 966 2.346541 TGAGCTGAGGTGAGCGGAG 61.347 63.158 0.00 0.00 44.24 4.63
680 967 2.283173 TGAGCTGAGGTGAGCGGA 60.283 61.111 0.00 0.00 44.24 5.54
681 968 2.125753 GTGAGCTGAGGTGAGCGG 60.126 66.667 0.00 0.00 44.24 5.52
682 969 2.125753 GGTGAGCTGAGGTGAGCG 60.126 66.667 0.00 0.00 44.24 5.03
683 970 1.217779 GAGGTGAGCTGAGGTGAGC 59.782 63.158 0.00 0.00 39.46 4.26
684 971 0.531657 CTGAGGTGAGCTGAGGTGAG 59.468 60.000 0.00 0.00 0.00 3.51
685 972 1.539560 GCTGAGGTGAGCTGAGGTGA 61.540 60.000 0.00 0.00 35.95 4.02
686 973 1.079266 GCTGAGGTGAGCTGAGGTG 60.079 63.158 0.00 0.00 35.95 4.00
687 974 3.386592 GCTGAGGTGAGCTGAGGT 58.613 61.111 0.00 0.00 35.95 3.85
837 1124 0.742990 CTTTAATGGCACGAGCGGGA 60.743 55.000 0.00 0.00 43.41 5.14
839 1126 1.721487 CCTTTAATGGCACGAGCGG 59.279 57.895 0.00 0.00 43.41 5.52
931 1228 4.759205 ATCCGCCCAAACCCCTGC 62.759 66.667 0.00 0.00 0.00 4.85
945 1242 1.641577 CCGTCTTGTTCCTCGAATCC 58.358 55.000 0.00 0.00 0.00 3.01
972 1270 1.935933 AATACCACGGCGAATCAGAC 58.064 50.000 16.62 0.00 0.00 3.51
1107 1405 4.154347 GAGGAGCTGGAGTGGCCG 62.154 72.222 0.00 0.00 40.66 6.13
1131 1432 2.422093 GGGAGGGAAGAAGGCTTACATG 60.422 54.545 0.00 0.00 36.63 3.21
1146 1447 0.041684 AGCAAGGAAATTGGGGAGGG 59.958 55.000 0.00 0.00 39.47 4.30
1155 1456 0.541296 AGCACCTGCAGCAAGGAAAT 60.541 50.000 8.66 1.12 45.16 2.17
1156 1457 1.152694 AGCACCTGCAGCAAGGAAA 60.153 52.632 8.66 0.00 45.16 3.13
1157 1458 1.601759 GAGCACCTGCAGCAAGGAA 60.602 57.895 8.66 0.00 45.16 3.36
1161 1462 0.752743 AAACAGAGCACCTGCAGCAA 60.753 50.000 8.66 0.00 46.81 3.91
1163 1464 1.578423 GAAACAGAGCACCTGCAGC 59.422 57.895 8.66 0.00 46.81 5.25
1164 1465 0.250640 AGGAAACAGAGCACCTGCAG 60.251 55.000 6.78 6.78 46.81 4.41
1166 1467 2.251600 CAGGAAACAGAGCACCTGC 58.748 57.895 0.00 0.00 46.81 4.85
1169 1489 0.250467 TCAGCAGGAAACAGAGCACC 60.250 55.000 0.00 0.00 0.00 5.01
1181 1501 4.553323 CAAGGAGAACAAAATTCAGCAGG 58.447 43.478 0.00 0.00 0.00 4.85
1197 1517 6.301169 AGACCAGACTAATTAACCAAGGAG 57.699 41.667 0.00 0.00 0.00 3.69
1224 1549 4.099113 TGAATTTTGATGTTCACTGCCACA 59.901 37.500 0.00 0.00 29.93 4.17
1225 1550 4.619973 TGAATTTTGATGTTCACTGCCAC 58.380 39.130 0.00 0.00 29.93 5.01
1226 1551 4.583907 TCTGAATTTTGATGTTCACTGCCA 59.416 37.500 0.00 0.00 31.55 4.92
1257 1583 1.873591 ACCAGAAAACAACTAGCAGCG 59.126 47.619 0.00 0.00 0.00 5.18
1273 1599 1.071471 AACCGGCTCTTCACACCAG 59.929 57.895 0.00 0.00 0.00 4.00
1288 1614 2.573915 AGGGGAGAGATTTGAGTCAACC 59.426 50.000 4.68 2.14 0.00 3.77
1290 1616 3.652869 ACAAGGGGAGAGATTTGAGTCAA 59.347 43.478 0.08 0.08 0.00 3.18
1294 1620 4.566426 AAGACAAGGGGAGAGATTTGAG 57.434 45.455 0.00 0.00 0.00 3.02
1299 1625 1.065854 CGCAAAGACAAGGGGAGAGAT 60.066 52.381 0.00 0.00 0.00 2.75
1301 1627 0.321671 TCGCAAAGACAAGGGGAGAG 59.678 55.000 0.00 0.00 0.00 3.20
1305 1631 1.243342 TGCATCGCAAAGACAAGGGG 61.243 55.000 0.00 0.00 34.76 4.79
1306 1632 0.169672 CTGCATCGCAAAGACAAGGG 59.830 55.000 0.00 0.00 38.41 3.95
1396 1722 1.153289 CCTCGTGAATCTGGGCCAG 60.153 63.158 28.01 28.01 0.00 4.85
1401 1727 0.179089 CCAGCTCCTCGTGAATCTGG 60.179 60.000 0.00 0.00 37.42 3.86
1608 1934 2.383527 GCACGAGCCAAGAAGGTCG 61.384 63.158 11.15 11.15 42.65 4.79
1824 2150 1.071071 TGTGACTCCTTAAACCCACCG 59.929 52.381 0.00 0.00 0.00 4.94
1869 2195 2.041620 GCCAATAGGGGAGATGCCATTA 59.958 50.000 0.00 0.00 38.95 1.90
1872 2198 0.992970 TGCCAATAGGGGAGATGCCA 60.993 55.000 0.00 0.00 38.95 4.92
1890 2216 1.321474 ATTTACTGATGGCCCGCATG 58.679 50.000 0.00 0.00 0.00 4.06
1953 2279 4.451629 AGCAAAATCAAGCATCTCCAAG 57.548 40.909 0.00 0.00 0.00 3.61
1980 2306 0.324943 TGAGGCCCTTACAGCAGAAC 59.675 55.000 0.00 0.00 0.00 3.01
2046 2372 4.940046 CACTCCATGTAATCTATGGCATCC 59.060 45.833 1.65 0.00 43.81 3.51
2164 2490 8.716539 TGCTTATTCGCAGAGGAGAATATCCG 62.717 46.154 2.54 0.00 42.70 4.18
2271 2597 2.656560 AGCTTACGGTGACATCTGAC 57.343 50.000 0.00 0.00 0.00 3.51
2319 2645 4.826556 ACAACTGCTTCTGTCTAGAATCC 58.173 43.478 0.00 0.00 41.83 3.01
2511 2837 0.599728 GAGGCCAGCGAGATGACATC 60.600 60.000 5.01 7.39 0.00 3.06
2523 2849 1.077212 CATCCACCCAAGAGGCCAG 60.077 63.158 5.01 0.00 40.58 4.85
2581 2907 6.041409 TCAGTAGCCTTATTGAGATTCTCCAG 59.959 42.308 11.12 2.52 0.00 3.86
3006 3332 7.816995 AGAAGTAGCAAAGATTGTCTGAAGTAG 59.183 37.037 0.00 0.00 0.00 2.57
3063 3389 9.727627 GCATTATGCCAGCTATTAATTATTCTC 57.272 33.333 5.80 0.00 37.42 2.87
3108 3435 9.394767 TGTGATGTAGCATCTACAATGTTAATT 57.605 29.630 10.29 0.00 0.00 1.40
3112 3439 6.261603 CCATGTGATGTAGCATCTACAATGTT 59.738 38.462 10.29 0.00 0.00 2.71
3113 3440 5.761726 CCATGTGATGTAGCATCTACAATGT 59.238 40.000 10.29 0.00 0.00 2.71
3159 3486 4.457257 GCCATCTACTGAATTAGCATTCCC 59.543 45.833 0.00 0.00 38.50 3.97
3265 3592 9.546428 ACAATTTAATCTGGAAAAAGAACCAAG 57.454 29.630 0.00 0.00 35.67 3.61
3268 3595 8.367911 AGGACAATTTAATCTGGAAAAAGAACC 58.632 33.333 0.00 0.00 0.00 3.62
3345 3672 5.088739 CCTTCATAAACAAGTCGTTCATGC 58.911 41.667 0.00 0.00 33.74 4.06
3354 3681 7.633789 ACAGTATCCATCCTTCATAAACAAGT 58.366 34.615 0.00 0.00 0.00 3.16
3363 3690 7.179160 CCAGTATCATACAGTATCCATCCTTCA 59.821 40.741 0.00 0.00 0.00 3.02
3426 3753 6.294010 CCTCAAATGATCTCTGTATGGCAATG 60.294 42.308 0.00 0.00 0.00 2.82
3605 3932 3.189287 GCATAGGAATGTTTATCCAGGCG 59.811 47.826 0.00 0.00 39.55 5.52
3623 3950 4.219070 GGCAGCAAATCCTTATCATGCATA 59.781 41.667 0.00 0.00 39.42 3.14
3721 4048 1.600916 GCGAGCCTGGGACAAAACT 60.601 57.895 0.00 0.00 38.70 2.66
3939 4266 1.429930 TGTTAGGAGCACCAGGACAA 58.570 50.000 2.07 0.00 38.94 3.18
3968 4295 6.406737 GGAGTACCCTCAATAGACCAGTTAAC 60.407 46.154 0.00 0.00 39.64 2.01
4134 4461 6.542370 GGCAGGTAGCTAAGATGATTACAAAA 59.458 38.462 0.00 0.00 44.79 2.44
4554 4882 3.015327 GACCATCTGCAGATCAGCTTTT 58.985 45.455 26.44 0.67 42.56 2.27
4775 5103 5.358725 ACTGGGTAGTTGGTTTGTTAAAGTG 59.641 40.000 0.00 0.00 31.66 3.16
4822 5150 7.492020 GCATAGAATATGGCAAACAACATTGAA 59.508 33.333 0.00 0.00 31.84 2.69
5085 5414 3.781770 GAGGGCGCCTGAGATGTCG 62.782 68.421 28.56 0.00 31.76 4.35
5261 5590 6.769608 AAACTAAAAATTACTGCTTGCTGC 57.230 33.333 0.00 0.00 43.25 5.25
5480 5810 4.193826 TGAAGTGGATCTTACAGCAGTC 57.806 45.455 0.00 0.00 36.40 3.51
5508 5838 7.966753 CGCAACAGATTCACTACTAAGTACTAA 59.033 37.037 0.00 0.00 33.48 2.24
5509 5839 7.335171 TCGCAACAGATTCACTACTAAGTACTA 59.665 37.037 0.00 0.00 33.48 1.82
5510 5840 6.150641 TCGCAACAGATTCACTACTAAGTACT 59.849 38.462 0.00 0.00 33.48 2.73
5511 5841 6.250951 GTCGCAACAGATTCACTACTAAGTAC 59.749 42.308 0.00 0.00 33.48 2.73
5512 5842 6.072342 TGTCGCAACAGATTCACTACTAAGTA 60.072 38.462 0.00 0.00 33.48 2.24
5513 5843 5.162075 GTCGCAACAGATTCACTACTAAGT 58.838 41.667 0.00 0.00 35.91 2.24
5514 5844 5.161358 TGTCGCAACAGATTCACTACTAAG 58.839 41.667 0.00 0.00 0.00 2.18
5635 5972 5.947228 ATCACACAAAGACAACTACATGG 57.053 39.130 0.00 0.00 0.00 3.66
5647 5984 7.415206 GCCCTAACCATAGTTAATCACACAAAG 60.415 40.741 0.00 0.00 37.99 2.77
6062 6410 9.371136 GTCATCAACAGAATCAAACACTAGATA 57.629 33.333 0.00 0.00 0.00 1.98
6073 6421 2.028203 TCGGCAGTCATCAACAGAATCA 60.028 45.455 0.00 0.00 0.00 2.57
6074 6422 2.621338 TCGGCAGTCATCAACAGAATC 58.379 47.619 0.00 0.00 0.00 2.52
6079 6427 2.844946 TCTTTTCGGCAGTCATCAACA 58.155 42.857 0.00 0.00 0.00 3.33
6126 6474 1.613255 GGCCAGATTTCTTGTTCCCGA 60.613 52.381 0.00 0.00 0.00 5.14


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.